Initial conformation of kinesin's neck linker

How ATP binding initiates the docking process of kinesin＇s neck linker is a key question in understanding kinesin mechanisms. By exploiting a molecular dynamics method, we investigate the initial conformation of kinesin＇s neck linker in its docking process. We find that, in the initial conformation, the neck linker has interactions with /30 and forms a ＇cover-neck bundle＇ structure with/30. From this initial structure, the formation of extra turns and the docking of the cover- neck bundle structure can be achieved. The motor head provides a forward force on the initial cover-neck bundle structure through ATP-induced rotation. This force, together with the hydrophobic interaction of ILE327 with the hydrophobic pocket on the motor head, drives the formation of the extra turn and initiates the neck linker docking process. Based on these findings, a pathway from ATP binding-induced motor head rotation to neck linker docking is proposed.     

生态系统的参数确定问题

通过不同观测数据研究捕食者—被捕食者生态系统参数确定问题.研究了四种情形1.观察数据无误差,并已知一个参数值.这种情况下,参数可由其相轨线和最小二乘法精确确定.2.观察数据无误差,但所有参数未知.此时仅靠相轨线的研究,无论给出多少组精确数据,都无法精确确定这些参数.通过原非线性模型的数值计算和网格搜索法,至少需要4组数据,同样得到了精度较高的参数值.3.当观测数据有误差时,根据解的周期性,引入标准周期的概念,在一个标准周期里讨论参数的确定问题,并利用标准周期内的捕食者与被捕食者的数量均值与系统的平衡点的关系对参数进行修正,然后使用网格法进行搜索,进一步提高了参数的精度.4.当观测时间也有误差时,先选取相对最优的随机正态数对观测时刻进行修正,然后再利用3.的方法估计参数.     

生物信息学与物理学

简要介绍了人类、模式生物基因组的测序计划以及生物大分子的数据库。并阐述了生物学的主要研究方向。     

布朗马达的非均匀高斯跃迁模型

提出了布朗马达的非均匀高斯跃迁理论，用布朗粒子在多态之间的跃迁模型描述分子马达的定向运动.假定跃迁速率与位置有关，且在跃迁点附近具有高斯函数形式，将布朗粒子在x处的概率密度Pm(x,t)在跃迁点附近展开，可以进行任意阶的近似计算.这一理论涵盖了以往的定点跃迁模型和均匀跃迁模型.作为具体例子，研究了系统在两态之间的跃迁问题.假定在一个周期内有两个跃迁点，讨论了布朗粒子定向运动产生的概率流随温度、跃迁速率和 跃迁宽度的变化关系. 关键词： 布朗马达 高斯跃迁 概率流     

Water in the Neck-Zipper Region of Kinesin

Neck linker （NL） is one of the most important mechanical elements of kinesin motors. The zipping up process of the neck-zipper （NZ） formed by NL and the related secondary structure elements is one of the major parts of kinesin＇s power stroke. All the weak interactions that are responsible for the formation of NZ are sensitive to or dependent on water. To investigate the role of water in the NZ region, a molecular dynamics （MD） model is set up with a crystal structure of kinesin 2KIN surrounded by a 10 A water layer, and minimization is performed to determine the positions of hydrogen atoms and other atoms. It is revealed that water molecules can assist the docking process of NL by forming hydrogen bonds at those positions where direct hydrogen bonding between the two sides of NZ is hindered and then acts as a constructive component of NZ at the docked state of NL. This result may improve the understanding of the mechanism for the docking of NL of kinesin wherein the function of water has not been comprehended sufficiently.     

K+离子通道及其研究进展

 细胞是通过细胞膜与外界隔离的,在细胞膜上有很多离子通道,细胞通过这些通道与外界进行离子交换。离子通道在许多细胞活动中都起关键作用,它是生物电活动的基础,在细胞内和细胞间信号传递中起着重要作用。离子通道通过调控细胞内pH值和离子浓度来维持正常的细胞体积及细胞内生物分子活性所需的离子浓度范围。特别是通过改变作为第二信使的钙离子浓度,来调控各种生化过程。生命的很多过程如发育、生长、分泌、兴奋、运动,甚至于学习和记忆都与离子通道功能的正常发挥有直接联系。目前,离子通道的研究已成为分子生物学、分子药理学、生物物理学、神经生物学等多种学科的热点。     

向生命学习新的机制

根据有关分子马达的重要实验结果,明确指出分子马达的运动过程是一个化学、电学、力学3种过程互相耦合的生物学过程。主要介绍有关kinesin的力产生机制的研究现状以及在这方面的研究。On the basis of the important experimental results of molecular motors, it was polnted out that the moving process of molecular motors is a coupling biological process of chemical-electrical-mechanical processes. This clever mechanism of energy conversion on the molecular level with several processes coupled together had never been observed before. The understanding of this new mechanism is an important step towards the understanding of life and an important content of what we can learn from life. We introduced here the status of the investigations on the mechanism for the force generation of kinesin and the studies of the authors in this field     

Protection-against-water-attack determined difference between strengths of backbone hydrogen bonds in kinesin's neck zipper region

Docking of the kinesin's neck linker(NL) to the motor domain is the key force-generation process of the kinesin.In this process, NL's β10 portion forms four backbone hydrogen bonds(HBs) with the motor domain. These backbone hydrogen bonds show big differences in their effective strength. The origins of these strength differences are still unclear.Using molecular dynamics method, we investigate the stability of the backbone HBs in explicit water environment. We find that the strength differences of these backbone HBs mainly arise from their relationships with water molecules which are controlled by arranging the surrounding residue sidechains. The arrangement of the residues in the C-terminal part of β10 results in the existence of the water-attack channels around the backbone HBs in this region. Along these channels the water molecules can directly attack the backbone HBs and make these HBs relatively weak. In contrast, the backbone HB at the N-terminus of β10 is protected by the surrounding hydrophobic and hydrophilic residues which cooperate positively with the central backbone HB and make this HB highly strong. The intimate relationship between the effective strength of protein backbone HB and water revealed here should be considered when performing mechanical analysis for protein conformational changes.     

驱动蛋白及其研究进展

 生命活动与体内的输运过程密切相关。像我们在宏观层次中用到的热机一样,在生物体内也存在着许多具有马达功能的微观“机器”--分子马达(molecularmotor)。它们广泛存在于肌肉纤维和细胞组织中,是一种特殊的蛋白质大分子。